The invasive monozoic tapeworm Atractolytocestus huronensis, a specific parasite of common carp, was originally found and described in the North American continent. It has been introduced to Europe and reported in several countries in the last 15 years, as well. In the current study, tapeworms from one North American (USA) and five European localities (United Kingdom/UK, Slovakia, Hungary, Croatia, and Romania) were subjected to molecular analyses in order to determine the level of intrapopulation and intraspecific molecular variation and to assess interrelationships among American and European populations of the parasite. Partial sequences (672 bp) of the mitochondrial cytochrome c oxidase subunit I (cox1) revealed the presence of only two cox1 haplotypes, in accordance with the nonnative character of the populations. The first haplotype was common for all tapeworms from the Continental Europe (Slovakia, Hungary, Croatia, and Romania); no differences were determined either within or among respective A. huronensis populations. The second cox1 haplotype was characterized in all individuals from the USA and UK, indicating their close genetic relationship. Both haplotypes differed in three nucleotide positions (99.6% identity) which did not change the amino acid sequence. The cox1 data imply that introduction of the parasite to Europe was probably the result of two independent events directed to the UK and Continental Europe. The very close genetic relationship between British and American A. huronensis was reflected also by similar ribosomal internal transcribed spacer 2 (ITS2) sequence structure; considerable intragenomic ITS2 variability was detected in all individuals of both geographic populations. Divergent ITS2 copies were mostly induced by different numbers of short repetitive motifs within the sequences, allowing their assortment into two ITS2 variants.